Theoretical and Applied Genetics

, Volume 109, Issue 6, pp 1295–1302 | Cite as

Genome-specific primer sets for starch biosynthesis genes in wheat

  • N. K. Blake
  • J. D. Sherman
  • J. Dvořák
  • L. E. Talbert
Original Paper


Common wheat (Triticum aestivum L., 2n=6x=42) is an allohexaploid composed of three closely related genomes, designated A, B, and D. Genetic analysis in wheat is complicated, as most genes are present in triplicated sets located in the same chromosomal regions of homoeologous chromosomes. The goal of this report was to use genomic information gathered from wheat–rice sequence comparison to develop genome-specific primer sets for five genes involved in starch biosynthesis. Intron locations in wheat were inferred through the alignment of wheat cDNA sequences with rice genomic sequence. Exon-anchored primers, which amplify across introns, allowed the sequencing of introns from the three genomes for each gene. Sequence variation within introns among the three wheat genomes provided the basis for genome-specific primer design. For three genes, ADP-glucose pyrophosphorylase (Agp-L), sucrose transporter (SUT), and waxy (Wx), genome-specific primer sets were developed for all three genomes. Genome-specific primers were developed for two of the three genomes for Agp-S and starch synthase I (SsI). Thus, 13 of 15 possible genome-specific primer sets were developed using this strategy. Seven genome-specific primer combinations were used to amplify alleles in hexaploid wheat lines for sequence comparison. Three single nucleotide polymorphisms (SNPs) were identified in a comparison of 5,093 bp among a minimum of ten wheat accessions. Two of these SNPs could be converted into cleaved amplified polymorphism sequence (CAPS) markers. Our results indicated that the design of genome-specific primer sets using intron-based sequence differences has a high probability of success, while the identification of polymorphism among alleles within a genome may be a challenge.


Hexaploid Wheat Rice Chromosome Cleave Amplify Polymorphic Sequence Wheat Genome Starch Biosynthesis 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This publication is based on work supported by the National Science Foundation Grant No. DBI0321757 and USDA-IFAFS Project No. 2001-52100-11293. The authors gratefully acknowledge the assistance of Jason Cook, Kelly Hansen, Megan Hartzell, and Steve Morris.


  1. Aoki N, Whitfeld P, Hoeren F, Scofield G, Newell K, Patrick J, Offler C, Clarke B, Rahman S, Furbank RT (2002) Three sucrose transporter genes are expressed in the developing grain of hexaploid wheat. Plant Mol Biol 50:453–462CrossRefPubMedGoogle Scholar
  2. Akhunov ED, Akhunov AR, Linkiewicz AM, Dubcovsky J, Hummel D, Lazo G, Chao S, Anderson OD, David J, Qi LL et al (2003) Synteny perturbations between wheat homoeologous chromosomes by locus duplications and deletions correlate with recombination rates along chromosome arms. Proc Natl Acad Sci USA 100:10836–10841CrossRefPubMedGoogle Scholar
  3. Blake NK, Lehfeldt BR, Lavin M, Talbert LE (1999) Phylogenetic reconstruction based on low copy DNA sequence analysis in an allopolyploid: the B genome of wheat. Genome 42:351–360CrossRefPubMedGoogle Scholar
  4. Bryan GJ, Stephenson P, Collins A, Kirby J, Smith JB, Gale MD (1999) Low levels of DNA sequence variation among adapted genotypes of hexaploid wheat. Theor Appl Genet 99:192–198CrossRefGoogle Scholar
  5. Chetelat RT, DeVerna JW, Bennett AB (1995) Introgression into tomato (Lycopersicon esculentum) of the L. chmielewskii sucrose accumulator gene (sucr) controlling fruit sugar composition. Theor Appl Genet 91:327–333Google Scholar
  6. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342–1353CrossRefPubMedGoogle Scholar
  7. Esen A, Bandaranayake H (1998) Insertional polymorphism in introns 4 and 10 of the maize-glucosidase gene glu1. Genome 41:597–604CrossRefPubMedGoogle Scholar
  8. Gill KS, Lubbers, EL, Gill BS, Raupp WJ, Cox TS (1991) A genetic linkage map of Triticum tauschii (DD) and its relationship to the D genome of bread wheat (AABBDD). Genome 34:362–374Google Scholar
  9. Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T (2002) Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190,562 genetic variations in the human genome. J Hum Genet 47:605–610CrossRefPubMedGoogle Scholar
  10. Hannah LC (1997) Starch synthesis in the maize seed. In: Larkins BA, Vasil IK (eds) Cellular and molecular biology of plant seed development. Kluwer, Dordrecht, pp 375–405Google Scholar
  11. Hongtrakul V, Slabaugh MB, Knapp SJ (1998) DFLP, SSCP, and SSR markers for delta 9-stearoyl-acyl carrier protein desaturases strongly expressed in developing seeds of sunflower: intron lengths are polymorphic among elite inbred lines. Mol Breed 4:195–203CrossRefGoogle Scholar
  12. Lemoine R (2000) Sucrose transporters in plants: update on function and structure. Biochim Biophys Acta 1465:246–262Google Scholar
  13. Murai J, Taira T, Ohta D (1999) Isolation and characterization of the three Waxy genes encoding the granule-bound starch synthase in hexaploid wheat. Gene 234:71–79CrossRefPubMedGoogle Scholar
  14. Pestsova E, Ganal MW, Röder MS (2000) Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43:689–697CrossRefPubMedGoogle Scholar
  15. Preiss J (1997) Modulation of starch synthesis. In: Foyer C-H, Quick W-P (eds) A molecular approach to primary metabolism in higher plants. Taylor and Francis, London, pp 81–104Google Scholar
  16. Preiss J, Sivak MN (1998) Biochemistry, molecular biology and regulation of starch synthesis. In: Setlow, JK (ed) Genetic engineering, principles and methods, vol 20. Plenum, New York, pp. 177–223Google Scholar
  17. Ramakrishna W, Dubcovsky J, Park YJ, Busso C, Embereton J, SanMiguel P, Bennetzen JL (2002) Different types and rates of genome evolution detected by comparative sequence analysis of orthologous segments from four cereal genomes. Genetics 162:1389–1400PubMedGoogle Scholar
  18. Röder MS, Plaschke J, Konig SU, Borner A, Sorrells ME, Tanksley SD, Ganal MW (1995) Abundance variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333PubMedGoogle Scholar
  19. Sears ER (1954) The aneuploids of common wheat. Mo Agric Exp Stn Res Bull 472 Google Scholar
  20. Shure M, Federoff N, Wessler S (1983) Molecular identification and isolation of the Waxy locus in maize Zea mays. Cell 35:225–233CrossRefPubMedGoogle Scholar
  21. Smidansky ED, Clancy M, Meyer FD, Lanning SP, Blake NK, Talbert LE, Giroux MJ (2002) Enhanced ADP-glucose pyrophosphorylase activity in wheat endosperm increase seed yield. Proc Natl Acad Sci USA 99:1724–1729CrossRefPubMedGoogle Scholar
  22. Smidansky ED, Martin JM, Hannah LC, Fischer AM, Giroux MJ (2003) Seed yield and plant biomass increases in rice are conferred by deregulation of endosperm ADP-glucose pyrophosphorylase. Planta 216:656–664PubMedGoogle Scholar
  23. Somers DJ, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 49:431–437CrossRefGoogle Scholar
  24. Talbert LE, Smith LY, Blake NK (1998) More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA. Genome 41:402–407CrossRefGoogle Scholar
  25. Van Campenhout S, Gebeyaw Z, Volckaert G (2003) Conversion of two RFLP probes to orthologue-specific STS-PCR markers and illustration of their applicability for comparative analysis of genome variation and relatedness in polyploidy wheat species. Proc Wheat Genet Symp 10:533–535Google Scholar
  26. Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES (2002) Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci USA 99:12959–12962CrossRefPubMedGoogle Scholar
  27. US Wheat and Barley Scab Initiative (2001)

Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • N. K. Blake
    • 1
  • J. D. Sherman
    • 1
  • J. Dvořák
    • 2
  • L. E. Talbert
    • 1
  1. 1.Plant Sciences DepartmentMontana State UniversityBozemanUSA
  2. 2.Department of Agronomy and Range ScienceUniversity of CaliforniaDavisUSA

Personalised recommendations